Giguet-Covex, Charline (2023): Plant DNA taxa detected in Lake La Thuile sediments (North-western Alps) over the last 6500 years [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.958680, In: Giguet-Covex, Charline; Chen, Wentao; Ficetola, Francesco Gentile; Gielly, Ludovic; Pansu, Johan (2023): Plant DNA analyses, nature and intensity of human activities, and erosion intensities in the North-western Alps over the last 4000-6000 years inferred from lake sediments [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.958732
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Related to:
Giguet-Covex, Charline; Bajard, Manon; Chen, Wentao; Walsh, Kevin; Rey, Pierre-Jérôme; Messager, Erwan; Etienne, David; Sabatier, Pierre; Ficetola, Francesco Gentile; Gielly, Ludovic; Blanchet, C; Guffond, Christophe; Chiquet, Patricia; Arnaud, Fabien; Poulenard, Jérôme (2023): Long-term trajectories of mountain agro-ecosystems in the North-Western Alps. Regional Environmental Change, 23(2), 58, https://doi.org/10.1007/s10113-023-02030-5
Funding:
European Commission (EC), grant/award no. 655331: agroPastoral Activities and effects on Landscapes and ErOsion dynAmics in the alps: a new insight from Geological appRoaches and lake sedIment DNA (PALEO-AGRI)
Coverage:
Latitude: 45.530587 * Longitude: 6.056265
Date/Time Start: 2010-04-26T00:00:00 * Date/Time End: 2010-04-26T00:00:00
Minimum Elevation: 874.0 m * Maximum Elevation: 874.0 m
Event(s):
Comment:
This dataset contains plant taxa detected by sedimentary DNA analyses. The dataset is presented in number of DNA sequences by replicate of analyses (4 PCR replicates for plants and 12 for mammals). It has been generated applying the DNA metabarcoding approach on a 5.49-m long sediment cores retrieved by using a UWITEC platform and coring devices. The primers used are g (5'-GGGCAATCCTGAGCCAA-3') and h (5'-CCATTGAGTCTCTGCACCTATC-3') (Taberlet, P., et al. Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucleic acids research, 35(3), e14-e14. (2007)). The sequences were then produced by the Illumina technology (HiSeq instrument). The bioinformatic treatment of the sequences was operated applying the Obitool program (Boyer, F. et al. OBITOOLS:aUNIX-inspired software package for DNAmetabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016)) and following the procedure described in Giguet-Covex et al. New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality. Scientific Reports. 9, 14676 (2019) (DOI https://doi.org/10.1038/s41598-019-50339-1). Further filtering treatments were then applied, as also described in Giguet-Covex et al. 2019. These second treatments allow the removal of 1) taxa assigned to a reference taxon at <95 % of sequence identity, 2) potential contaminations (based on sampling, extraction and PCR controls, and recognition of exotic taxa) and 3) stochastic detections.
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | AGE | Age | ka BP | Giguet-Covex, Charline | Geocode | |
| 2 | Abies | Abi | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 3 | Acer | Ace | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 4 | Achillea | Ach | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 5 | Alnus | Aln | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 6 | Apiaceae | Apiae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 7 | Aquifoliaceae | Aquifoliaceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 8 | Arctostaphylos uva-ursi | Arc.u-u | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 9 | Asteraceae | Astae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 10 | Athyrium vidalii | A. vidalii | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 11 | Betulaceae | Betaea | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 12 | Caltha | Clh | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 13 | Cannabis sativa | Can.s | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 14 | Carex | Cax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 15 | Cladium | Cla | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 16 | Clematis afoliata | C. afoliata | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 17 | Convolvulaceae | Conae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 18 | Eudicotyledons | Eudicotyledons | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 19 | Cupressaceae | Cupae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 20 | Equisetum | Equ | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 21 | Fagaceae | Fagaceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 22 | Fagus | Fag | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 23 | Filipendula ulmaria | Flp.u | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 24 | Frangula | Frg | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 25 | Hedysareae | Hedysareae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 26 | Helianthemum nummularium | Hel.n | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 27 | Juglandaceae | Jugae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 28 | Knautia | Kna | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 29 | Lamiaceae | Lamae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 30 | Lathyrus pratensis | L. pratensis | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 31 | Lysimachia | Lys | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 32 | Maleae | Maleae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 33 | Medicago minima | M. minima | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 34 | Mentha | Men | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 35 | Mentheae | Mentheae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 36 | Picea | Pic | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 37 | Plantago | Pla | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 38 | Poeae | Poeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 39 | Polygonoideae | Polygonoideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 40 | Polygonum | Pol | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 41 | Polypodium vulgare | Ppd.v | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 42 | Pooideae | Pooideae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 43 | Potentilleae | Potentilleae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 44 | Prunus | Prn | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 45 | Pyrus | Yus | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 46 | Quercus | Que | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 47 | Ranunculaceae | Ranae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 48 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 49 | Ranunculus | Ran | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 50 | Rosa | Ros | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 51 | Rosodae | Rosodae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 52 | Rumex | Rum | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 53 | Salicaceae | Salicaceae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 54 | Sanguisorbinae | Sanguisorbinae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 55 | Saxifraga | Sax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 56 | Taxus | Tax | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 57 | Tilia | Til | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 58 | Trifolium | Tri | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 59 | Ulmaceae | Ulmeae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 60 | Urtica dioica | Urt.d | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 61 | Vaccinieae | Vaccinieae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 62 | Valeriana | Val | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 63 | Veronica | Ver | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 64 | Veronica alpina | V. alpina | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 65 | Viburnum lantana | Vib.l | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 66 | Viburnum opulus | Vib.o | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 67 | Vicia faba | Vic.f | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
| 68 | Vitaceae | Viteae | # | Giguet-Covex, Charline | DNA metabarcoding approach, gh primers | Number of DNA sequences by replicate of analyses |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
13400 data points
Download Data
View dataset as HTML (shows only first 2000 rows)